Generated banner for Human Protein Atlas Database
Generated logo for Human Protein Atlas Database

Human Protein Atlas Database

Google DeepMindOfficialPublished by Google DeepMind

  • Skill
  • Tool integration
  • Science and research
  • Apache-2.0
  • Low risk
  • Has scripts

From the author

Use when you want to retrieve semi-quantitative protein expression and spatial localisation data from the Human Protein Atlas (HPA).
— the description by Google DeepMind

AutoGineer summary

Written by AutoGineer from the skill’s own files, not by the author

The Human Protein Atlas (HPA) database integration allows researchers to access semi-quantitative protein expression data derived from immunohistochemistry (IHC) across normal human tissues and cancer types. This tool bridges the gap between transcriptomic data and actual protein presence, providing insights into subcellular localization and systemic protein abundance. It requires the use of a provided CLI wrapper to ensure fair usage and proper data handling.

What it does

  • Maps standard gene symbols to Ensembl IDs for database queries.
  • Retrieves semi-quantitative protein expression levels in specific human tissues.
  • Identifies subcellular organelles and structures where a protein is localized.
  • Fetches comprehensive metadata entries for specific genes.
  • Performs advanced searches based on expression criteria and specificity categories.

When to use it

  • When you need to confirm if a protein product exists for a specific gene.
  • When investigating the subcellular localization of a protein within a cell.
  • When comparing RNA-seq consensus data with actual protein expression levels.
  • When filtering for genes based on tissue-specific or brain-region-specific expression patterns.

Advantages

  • Provides protein-level validation beyond simple mRNA transcription data.
  • Standardizes queries through a robust CLI wrapper.
  • Supports complex filtering via the HPA search query syntax.
  • Automates the retrieval of large-scale biological datasets into JSON format.

Usage examples

“Get the Ensembl ID for the TP53 gene.”
The agent executes the resolve-ensembl-id command to map the symbol to its corresponding Ensembl ID, saving the result to a JSON file.
“Where is the protein encoded by ENSG00000141736 located within the cell?”
The agent uses the get-subcellular-location command to retrieve and report the specific organelles or structures associated with the protein.
“Find genes that are enriched in the amygdala.”
The agent uses the search-hpa command with the query 'brain_category_rna:amygdala' to return a list of matching genes.

Install

  1. Download the skill as a ZIP:

    https://mp-staging.autogineer.com/agent-skills/google-deepmind/human-protein-atlas-database/download
  2. Unzip it into the cross-client skills folder of your project:

    mkdir -p .agents/skills && unzip human-protein-atlas-database.zip -d .agents/skills

Documentation by Google DeepMind

Human Protein Atlas (HPA) Database Integration

This skill provides semi-quantitative protein expression and spatial localisation data from the Human Protein Atlas (HPA). While RNA-seq (e.g., GTEx) tells us if a gene is being transcribed, HPA confirms if the protein product actually exists, where it is located within the cell (e.g. nucleus vs cytoplasm), and its concentration in systemic blood circulation. The data is based on Immunohistochemistry (IHC) across normal human tissues and cancer types.

Prerequisites

  1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.

  2. User Notification: If .licenses/human_protein_atlas_database_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://www.proteinatlas.org/about/licence, then (2) create the file recording the notification text and timestamp.

When to Use

Use this skill when you need to:

  • Map a gene symbol to its Ensembl ID for HPA queries.

  • Retrieve the semi-quantitative protein abundance in normal human tissues and cancer types based on IHC staining (High, Medium, Low, or Not Detected).

  • Find the specific organelles or subcellular structures where a protein has been localized (e.g., nucleoplasm, mitochondria).

  • Check the consistency/agreement between RNA-seq consensus and protein expression levels.

  • Search for genes based on specific protein expression criteria (e.g., "elevated in amygdala" or "secreted proteins").

Do NOT use when you need to:

  • Query eQTLs, pQTLs, or any variant-level associations. HPA provides wild-type expression data and knows nothing about QTLs.

  • Query gene expression in non-human species. HPA is strictly for human proteins.

  • Retrieve purely quantitative RNA expression without interest in the protein product (consider using the GTEx skill instead).

Command Selection Guide

Pick the right command on the first try. Match the user's input to the correct subcommand below.

  • Map a gene symbol to Ensembl ID: resolve-ensembl-id

  • Get tissue protein expression levels: get-tissue-expression

  • Get subcellular location of a protein: get-subcellular-location

  • Get the full HPA metadata entry for a gene: get-atlas-entry

  • Search HPA for genes matching specific criteria: search-hpa

Quick Start

# Map the ERBB2 gene symbol to its Ensembl ID
uv run scripts/hpa_cli.py resolve-ensembl-id ERBB2 --output /tmp/erbb2_id.json

# Get subcellular location by Ensembl ID
uv run scripts/hpa_cli.py get-subcellular-location ENSG00000141736 --output /tmp/erbb2_location.json

All subcommands write JSON to disk. Always save output in the /tmp/ directory. The default output file is /tmp/hpa_output.json if --output is not specified.

Commands

1. resolve-ensembl-id — Gene Symbol → Ensembl ID

Maps a common gene symbol (e.g., "TP53", "ERBB2") to its Ensembl gene ID. HPA endpoints are strictly Ensembl-based.

uv run scripts/hpa_cli.py resolve-ensembl-id TP53 --output /tmp/tp53_id.json

Arguments:

  • gene_symbol (positional): The standard gene symbol (e.g., "TP53").

  • --output: Output file path (default: /tmp/hpa_output.json).

2. get-tissue-expression — Get Tissue Protein Levels

Returns a list of tissues and their corresponding protein expression levels (High, Medium, Low, or Not Detected) based on IHC staining.

uv run scripts/hpa_cli.py get-tissue-expression ENSG00000130234 \
  --tissues "duodenum,thyroid gland" --output /tmp/tissue_expr.json

Arguments:

  • ensembl_id (positional): The Ensembl Gene ID.

  • --tissues: Comma-separated list of tissues to filter by (optional, defaults to all available tissues).

  • --output: Output file path (default: /tmp/hpa_output.json).

3. get-subcellular-location — Get Subcellular Location

Retrieves the specific organelles or cellular structures where the protein has been localized.

uv run scripts/hpa_cli.py get-subcellular-location ENSG00000141736 \
  --output /tmp/subcellular.json

Arguments:

  • ensembl_id (positional): The Ensembl Gene ID.

  • --output: Output file path.

4. get-atlas-entry — Get Full HPA Entry

Fetches the full metadata for a gene, including IHC scores, RNA-seq consensus, and subcellular location.

uv run scripts/hpa_cli.py get-atlas-entry ENSG00000254647 \
  --output /tmp/ins_entry.json

Arguments:

  • ensembl_id (positional): The Ensembl Gene ID.

  • --format: Format of the returned entry, e.g., json (default: json).

  • --output: Output file path.

5. search-hpa — Search by Attribute

Allows filtering for genes based on specific criteria (e.g., "elevated in amygdala").

uv run scripts/hpa_cli.py search-hpa \
  --query "brain_category_rna:amygdala" \
  --output /tmp/search_results.json

Arguments:

  • --query: The search query string. Refer to references/search-api.md for details.

  • --output: Output file path.

Core Rules

  • Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce fair use and implement retry logic.

  • Notification: If this skill is used, ensure this is mentioned in the output.

API Versioning

The HPA website at www.proteinatlas.org always serves the latest data release. Older archived versions can be accessed via vNN.proteinatlas.org (e.g., v24.proteinatlas.org), while the current version's subdomain redirects to www.proteinatlas.org. This skill's scripts query the latest version by default.

Common Errors

  • If no results are returned, confirm the query is detailed enough starting with the api reference in references/search-api.md

  • If you cannot find the results, search the web for example HPA queries and use these to construct a better query.

  • The output is usually large. Use jq or write your own python data parsing library to process the search results. Never output to stdout, or cat the output file.

Files

LICENSE


                                 Apache License
                           Version 2.0, January 2004
                        http://www.apache.org/licenses/

   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION

   1. Definitions.

      "License" shall mean the terms and conditions for use, reproduction,
      and distribution as defined by Sections 1 through 9 of this document.

      "Licensor" shall mean the copyright owner or entity authorized by
      the copyright owner that is granting the License.

      "Legal Entity" shall mean the union of the acting entity and all
      other entities that control, are controlled by, or are under common
      control with that entity. For the purposes of this definition,
      "control" means (i) the power, direct or indirect, to cause the
      direction or management of such entity, whether by contract or
      otherwise, or (ii) ownership of fifty percent (50%) or more of the
      outstanding shares, or (iii) beneficial ownership of such entity.

      "You" (or "Your") shall mean an individual or Legal Entity
      exercising permissions granted by this License.

      "Source" form shall mean the preferred form for making modifications,
      including but not limited to software source code, documentation
      source, and configuration files.

      "Object" form shall mean any form resulting from mechanical
      transformation or translation of a Source form, including but
      not limited to compiled object code, generated documentation,
      and conversions to other media types.

      "Work" shall mean the work of authorship, whether in Source or
      Object form, made available under the License, as indicated by a
      copyright notice that is included in or attached to the work
      (an example is provided in the Appendix below).

      "Derivative Works" shall mean any work, whether in Source or Object
      form, that is based on (or derived from) the Work and for which the
      editorial revisions, annotations, elaborations, or other modifications
      represent, as a whole, an original work of authorship. For the purposes
      of this License, Derivative Works shall not include works that remain
      separable from, or merely link (or bind by name) to the interfaces of,
      the Work and Derivative Works thereof.

      "Contribution" shall mean any work of authorship, including
      the original version of the Work and any modifications or additions
      to that Work or Derivative Works thereof, that is intentionally
      submitted to Licensor for inclusion in the Work by the copyright owner
      or by an individual or Legal Entity authorized to submit on behalf of
      the copyright owner. For the purposes of this definition, "submitted"
      means any form of electronic, verbal, or written communication sent
      to the Licensor or its representatives, including but not limited to
      communication on electronic mailing lists, source code control systems,
      and issue tracking systems that are managed by, or on behalf of, the
      Licensor for the purpose of discussing and improving the Work, but
      excluding communication that is conspicuously marked or otherwise
      designated in writing by the copyright owner as "Not a Contribution."

      "Contributor" shall mean Licensor and any individual or Legal Entity
      on behalf of whom a Contribution has been received by Licensor and
      subsequently incorporated within the Work.

   2. Grant of Copyright License. Subject to the terms and conditions of
      this License, each Contributor hereby grants to You a perpetual,
      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
      copyright license to reproduce, prepare Derivative Works of,
      publicly display, publicly perform, sublicense, and distribute the
      Work and such Derivative Works in Source or Object form.

   3. Grant of Patent License. Subject to the terms and conditions of
      this License, each Contributor hereby grants to You a perpetual,
      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
      (except as stated in this section) patent license to make, have made,
      use, offer to sell, sell, import, and otherwise transfer the Work,
      where such license applies only to those patent claims licensable
      by such Contributor that are necessarily infringed by their
      Contribution(s) alone or by combination of their Contribution(s)
      with the Work to which such Contribution(s) was submitted. If You
      institute patent litigation against any entity (including a
      cross-claim or counterclaim in a lawsuit) alleging that the Work
      or a Contribution incorporated within the Work constitutes direct
      or contributory patent infringement, then any patent licenses
      granted to You under this License for that Work shall terminate
      as of the date such litigation is filed.

   4. Redistribution. You may reproduce and distribute copies of the
      Work or Derivative Works thereof in any medium, with or without
      modifications, and in Source or Object form, provided that You
      meet the following conditions:

      (a) You must give any other recipients of the Work or
          Derivative Works a copy of this License; and

      (b) You must cause any modified files to carry prominent notices
          stating that You changed the files; and

      (c) You must retain, in the Source form of any Derivative Works
          that You distribute, all copyright, patent, trademark, and
          attribution notices from the Source form of the Work,
          excluding those notices that do not pertain to any part of
          the Derivative Works; and

      (d) If the Work includes a "NOTICE" text file as part of its
          distribution, then any Derivative Works that You distribute must
          include a readable copy of the attribution notices contained
          within such NOTICE file, excluding those notices that do not
          pertain to any part of the Derivative Works, in at least one
          of the following places: within a NOTICE text file distributed
          as part of the Derivative Works; within the Source form or
          documentation, if provided along with the Derivative Works; or,
          within a display generated by the Derivative Works, if and
          wherever such third-party notices normally appear. The contents
          of the NOTICE file are for informational purposes only and
          do not modify the License. You may add Your own attribution
          notices within Derivative Works that You distribute, alongside
          or as an addendum to the NOTICE text from the Work, provided
          that such additional attribution notices cannot be construed
          as modifying the License.

      You may add Your own copyright statement to Your modifications and
      may provide additional or different license terms and conditions
      for use, reproduction, or distribution of Your modifications, or
      for any such Derivative Works as a whole, provided Your use,
      reproduction, and distribution of the Work otherwise complies with
      the conditions stated in this License.

   5. Submission of Contributions. Unless You explicitly state otherwise,
      any Contribution intentionally submitted for inclusion in the Work
      by You to the Licensor shall be under the terms and conditions of
      this License, without any additional terms or conditions.
      Notwithstanding the above, nothing herein shall supersede or modify
      the terms of any separate license agreement you may have executed
      with Licensor regarding such Contributions.

   6. Trademarks. This License does not grant permission to use the trade
      names, trademarks, service marks, or product names of the Licensor,
      except as required for reasonable and customary use in describing the
      origin of the Work and reproducing the content of the NOTICE file.

   7. Disclaimer of Warranty. Unless required by applicable law or
      agreed to in writing, Licensor provides the Work (and each
      Contributor provides its Contributions) on an "AS IS" BASIS,
      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
      implied, including, without limitation, any warranties or conditions
      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
      PARTICULAR PURPOSE. You are solely responsible for determining the
      appropriateness of using or redistributing the Work and assume any
      risks associated with Your exercise of permissions under this License.

   8. Limitation of Liability. In no event and under no legal theory,
      whether in tort (including negligence), contract, or otherwise,
      unless required by applicable law (such as deliberate and grossly
      negligent acts) or agreed to in writing, shall any Contributor be
      liable to You for damages, including any direct, indirect, special,
      incidental, or consequential damages of any character arising as a
      result of this License or out of the use or inability to use the
      Work (including but not limited to damages for loss of goodwill,
      work stoppage, computer failure or malfunction, or any and all
      other commercial damages or losses), even if such Contributor
      has been advised of the possibility of such damages.

   9. Accepting Warranty or Additional Liability. While redistributing
      the Work or Derivative Works thereof, You may choose to offer,
      and charge a fee for, acceptance of support, warranty, indemnity,
      or other liability obligations and/or rights consistent with this
      License. However, in accepting such obligations, You may act only
      on Your own behalf and on Your sole responsibility, not on behalf
      of any other Contributor, and only if You agree to indemnify,
      defend, and hold each Contributor harmless for any liability
      incurred by, or claims asserted against, such Contributor by reason
      of your accepting any such warranty or additional liability.

   END OF TERMS AND CONDITIONS

   APPENDIX: How to apply the Apache License to your work.

      To apply the Apache License to your work, attach the following
      boilerplate notice, with the fields enclosed by brackets "[]"
      replaced with your own identifying information. (Don't include
      the brackets!)  The text should be enclosed in the appropriate
      comment syntax for the file format. We also recommend that a
      file or class name and description of purpose be included on the
      same "printed page" as the copyright notice for easier
      identification within third-party archives.

   Copyright [yyyy] [name of copyright owner]

   Licensed under the Apache License, Version 2.0 (the "License");
   you may not use this file except in compliance with the License.
   You may obtain a copy of the License at

       http://www.apache.org/licenses/LICENSE-2.0

   Unless required by applicable law or agreed to in writing, software
   distributed under the License is distributed on an "AS IS" BASIS,
   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   See the License for the specific language governing permissions and
   limitations under the License.

Requirements and compatibility

Works with: Claude Code, Claude apps, OpenAI Codex, GitHub Copilot, Cursor, Gemini CLI, Kiro, OpenCode, Goose, Amp, Roo Code, JetBrains Junie, Factory Droid, Devin (ex-Windsurf), Mistral Vibe, OpenHands, Letta

“Works with” means the tool reads the open Agent Skills format; a skill written for one tool may use features others lack.

Needs: Needs Python

Security

What our scanner noticed· Low risk

  • Scripts that your agent may run

This skill includes scripts that your agent may run. Read them before you use it.

A static scan is not a guarantee. Skills are third-party content: review a skill before you let an agent use it.

Attribution and licence

Published by
Google DeepMind
Publisher
Google DeepMind (Official)
Source
google-deepmind/science-skills · skills/human_protein_atlas_database · commit 4de6786
Licence
Apache License 2.0 (redistribution allowed)
  • LICENSE (added by AutoGineer from LICENSE)
  • ATTRIBUTION.md (written by AutoGineer)
Synced

AutoGineer is not affiliated with or endorsed by Google DeepMind.

Download ZIP

The ZIP holds the skill’s files, its licence files and an ATTRIBUTION.md. Download human-protein-atlas-database.zip